NAME
unicycler_scrub - read trimming, chimera detection and misassembly detection
SYNOPSIS
unicycler_scrub [-h] -i INPUT -o OUT [-r READS] [--trim TRIM] [--split SPLIT] [--min_split_size MIN_SPLIT_SIZE] [--discard_chimeras] [-t THREADS] [--keep_paf] [--parameters PARAMETERS] [--verbosity VERBOSITY]
DESCRIPTION
Unicycler-scrub - read trimming, chimera detection and misassembly detection
OPTIONS
- -h, --help
-
show this help message and exit
- -i INPUT, --input INPUT
-
These are the reads or assembly to be scrubbed (can be FASTA or FASTQ format
- -o OUT, --out OUT
-
The scrubbed reads or assembly will be saved to this file (will have the same format as the --input file format) or use "none" to not produce an output file
- -r READS, --reads READS
-
These are the reads used to scrub --input (can be FASTA or FASTQ format) (default: same file as --input)
- --trim TRIM
-
The aggressiveness with which the input will be trimmed (0 to 100, where 0 is no trimming and 100 is very aggressive trimming) (default: 50)
- --split SPLIT
-
The aggressiveness with which the input will be split (0 to 100, where 0 is no splitting and 100 is very aggressive splitting) (default: 50)
- --min_split_size MIN_SPLIT_SIZE
-
Parts of split sequences will only be outputted if they are at least this big (default: 1000)
- --discard_chimeras
-
If used, chimeric sequences will be discarded instead of split (default: False)
- -t THREADS, --threads THREADS
-
Number of threads used (default: 4)
- --keep_paf
-
Save the alignments to file (makes repeated runs faster because alignments can be loaded from file) (default: False)
- --parameters PARAMETERS
-
Low-level parameters (for debugging use only) (default: )
- --verbosity VERBOSITY
-
Level of stdout information (default: 1)
-
0 = no stdout,
-
1 = basic progress indicators,
-
2 = extra info,
-
3 = debugging info
SEE ALSO
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.